4Z3K
Human sepiapterin reductase in complex with the cofactor NADP+ and the trypthophan metabolite xanthurenic acid
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4HWK |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 277 | 2% W/V PEG1000, 1.9 M Ammonium sulfate, 0.1 M Hepes pH7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.89 | 74.86 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 143.964 | α = 90 |
b = 143.964 | β = 90 |
c = 180.74 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 2M-F | 2014-11-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 1.00000 | SLS | X06DA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||
1 | 2.35 | 124.676 | 100 | 0.106 | 0.111 | 0.031 | 20 | 12.9 | 88165 | 88165 | 57.3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.35 | 2.48 | 100 | 1.085 | 1.085 | 0.307 | 0.7 | 13.3 | 12862 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4HWK | 2.35 | 124.676 | 83471 | 4633 | 99.99 | 0.1825 | 0.1808 | 0.2139 | RANDOM | 50.093 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.83 | 0.41 | 0.83 | -2.68 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.316 |
r_dihedral_angle_4_deg | 20.15 |
r_dihedral_angle_3_deg | 13.857 |
r_dihedral_angle_1_deg | 6.388 |
r_mcangle_it | 6.24 |
r_mcbond_it | 4.453 |
r_mcbond_other | 4.451 |
r_angle_refined_deg | 1.446 |
r_angle_other_deg | 0.732 |
r_chiral_restr | 0.085 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7744 |
Nucleic Acid Atoms | |
Solvent Atoms | 160 |
Heterogen Atoms | 286 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |